test(#6092): Add Pixi environment support

- Introduced PixiConfig and PixiCache classes for managing Pixi environments.
- Updated Session class to include PixiConfig retrieval.
- Enhanced CmdRun with options to enable/disable Pixi environments.
- Modified ConfigBuilder to apply Pixi environment settings based on command-line options.
- Updated BashWrapperBuilder to include Pixi activation in the execution script.
- Added pixiEnv property to TaskBean and methods in TaskRun for Pixi environment handling.
- Updated ProcessConfig to include 'pixi' in process configuration options.

This commit integrates Pixi environment management into the Nextflow framework, allowing users to specify and control Pixi environments during execution.

Signed-off-by: Edmund Miller <[email protected]>

Author: edmundmiller

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -68,6 +68,7 @@ import nextflow.script.ScriptFile
 import nextflow.script.ScriptMeta
 import nextflow.script.ScriptRunner
 import nextflow.script.WorkflowMetadata
+import nextflow.pixi.PixiConfig
 import nextflow.spack.SpackConfig
 import nextflow.trace.AnsiLogObserver
 import nextflow.trace.TraceObserver
@@ -1195,6 +1196,12 @@ class Session implements ISession {
         return new SpackConfig(opts, getSystemEnv())
     }
 
+    @Memoized
+    PixiConfig getPixiConfig() {
+        final cfg = config.pixi as Map ?: Collections.emptyMap()
+        return new PixiConfig(cfg, getSystemEnv())
+    }
+
     /**
      * Get the container engine configuration for the specified engine. If no engine is specified
      * if returns the one enabled in the configuration file. If no configuration is found

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -250,6 +250,12 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-without-spack'], description = 'Disable the use of Spack environments')
     Boolean withoutSpack
 
+    @Parameter(names=['-with-pixi'], description = 'Use the specified Pixi environment package or file (must end with .toml suffix)')
+    String withPixi
+
+    @Parameter(names=['-without-pixi'], description = 'Disable the use of Pixi environments')
+    Boolean withoutPixi
+
     @Parameter(names=['-offline'], description = 'Do not check for remote project updates')
     boolean offline = System.getenv('NXF_OFFLINE')=='true'
 

modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy

@@ -190,7 +190,7 @@ class ConfigBuilder {
 
         def result = []
         if ( files ) {
-            for( String fileName : files ) { 
+            for( String fileName : files ) {
                 def thisFile = currentDir.resolve(fileName)
                 if(!thisFile.exists()) {
                     throw new AbortOperationException("The specified configuration file does not exist: $thisFile -- check the name or choose another file")
@@ -594,6 +594,19 @@ class ConfigBuilder {
             config.spack.enabled = true
         }
 
+        if( cmdRun.withoutPixi && config.pixi instanceof Map ) {
+            // disable pixi execution
+            log.debug "Disabling execution with Pixi as requested by command-line option `-without-pixi`"
+            config.pixi.enabled = false
+        }
+
+        // -- apply the pixi environment
+        if( cmdRun.withPixi ) {
+            if( cmdRun.withPixi != '-' )
+                config.process.pixi = cmdRun.withPixi
+            config.pixi.enabled = true
+        }
+
         // -- sets the resume option
         if( cmdRun.resume )
             config.resume = cmdRun.resume
@@ -861,7 +874,7 @@ class ConfigBuilder {
             final value = entry.value
             final previous = getConfigVal0(config, key)
             keys << entry.key
-            
+
             if( previous==null ) {
                 config[key] = value
             }

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -341,6 +341,7 @@ class BashWrapperBuilder {
         binding.before_script = getBeforeScriptSnippet()
         binding.conda_activate = getCondaActivateSnippet()
         binding.spack_activate = getSpackActivateSnippet()
+        binding.pixi_activate = getPixiActivateSnippet()
 
         /*
          * add the task environment
@@ -394,7 +395,7 @@ class BashWrapperBuilder {
         binding.fix_ownership = fixOwnership() ? "[ \${NXF_OWNER:=''} ] && (shopt -s extglob; GLOBIGNORE='..'; chown -fR --from root \$NXF_OWNER ${workDir}/{*,.*}) || true" : null
 
         binding.trace_script = isTraceRequired() ? getTraceScript(binding) : null
-        
+
         return binding
     }
 
@@ -560,6 +561,29 @@ class BashWrapperBuilder {
         return result
     }
 
+    private String getPixiActivateSnippet() {
+        if( !pixiEnv )
+            return null
+        def result = "# pixi environment\n"
+
+        // Check if there's a .pixi file that points to the project directory
+        final pixiFile = pixiEnv.resolve('.pixi')
+        if( pixiFile.exists() ) {
+            // Read the project directory path
+            final projectDir = pixiFile.text.trim()
+            result += "cd ${Escape.path(projectDir as String)} && "
+            result += "eval \"\$(pixi shell-hook --shell bash)\" && "
+            result += "cd \"\$OLDPWD\"\n"
+        }
+        else {
+            // Direct activation from environment directory
+            result += "cd ${Escape.path(pixiEnv)} && "
+            result += "eval \"\$(pixi shell-hook --shell bash)\" && "
+            result += "cd \"\$OLDPWD\"\n"
+        }
+        return result
+    }
+
     protected String getTraceCommand(String interpreter) {
         String result = "${interpreter} ${fileStr(scriptFile)}"
         if( input != null )
@@ -628,7 +652,7 @@ class BashWrapperBuilder {
     private String copyFileToWorkDir(String fileName) {
         copyFile(fileName, workDir.resolve(fileName))
     }
-    
+
 
     String getCleanupCmd(String scratch) {
         String result = ''